[gmx-users] Free Energy Landscape- PCA

[Romero, Raquel]

Thanks a lot for your reply, Justin. That’s exactly what want but my problem is that don’t know how, I mean, how can I know that correspondence? Getting that correspondence is my only problem




> On 14 Dec 2016, at 12:49, Justin Lemkul <jalemkul at vt.edu> wrote:
> 
> 
> 
> On 12/12/16 9:30 AM, Romero, Raquel wrote:
>> Hi everyone,
>> 
>> 
>> I have a number of trajectories over which I have conducted PCA using Gromacs. I have also generated a Free Energy Landscape using g_sham when the trajectory is projected along the PCs. I would like to know how I can extract the coordinates of those states of minimum energy shown in the FEL.
>> 
> 
> You'll need to find the corresponding frames by matching the eigenvalues from the time series.  Then you can dump out those frames using trjconv -dump.
> 
> -Justin
> 
>> 
>> Thanks in advance,
>> 
>> 
>> Regards
>> 
>> 
>> 
>> Raquel Romero
>> Department of Pharmaceutical and Biological Chemistry
>> UCL School of Pharmacy, University College London
>> 29/39 Brunswick Square
>> London
>> WC1N 1AX
>> 
>> T: 0207 753 5972
>> E: raquel.romero.12 at ucl.ac.uk
>> 
> 
> -- 
> ==================================================
> 
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> 
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
> 
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
> 
> ==================================================
> -- 
> Gromacs Users mailing list
> 
> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
> 
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> 
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.